Thursday, June 27, 2013

Open Access - an insider's view

This is my mum's (Alice Meadows') response to my post on Open Access. She works for Wiley.

Your post hits on many of the key issues in open access (OA) and also raises some interesting points.

You are quite right that scientists may choose to publish OA so that more people can access their research. However, although it does seem to be true - unsurprisingly! - that OA articles are downloaded more and reach a broader audience, it is not yet clear that this leads to more citations. There have been several studies of this including one by my fellow Scholarly Kitchen blogger, Phil Davis, which indicate that OA articles are not, in fact, cited more. This could well change in future, of course, especially as more - and better - OA journals are launched. But for now the jury is out…

You are also right to point out that paying to publish will not necessarily lead to reduced costs for institutions (and I say institutions rather than libraries advisedly - it is by no means certain that this budget would stay within the library).  Your back-of-the-envelope calculation about the cost to UMass of moving to a fully 'gold' model (where you pay an article publication charge or APC, like PLoS) is echoed by, for example, the University of Oxford which has calculated that the APC costs for all its research output would likely exceed its current subscription costs (and would certainly exceed the amount it receives in its block grant from the Research Councils UK for APCs).  Other, less research intensive institutions, would certainly benefit financially from a move to Gold OA though - as would commercial organizations, such as pharmaceutical companies, who would have free access to large amounts of research that they currently have to pay for. There is also an alternative to gold OA; green OA permits an author to make a version of her/his article freely available in a repository, such as PubMedCentral, typically after an embargo period of somewhere between 6-24 months.

Both versions of OA have their pros and cons.  Gold OA acknowledges that there is a cost to publishing, which is a good thing - not just from my perspective as a publisher, but from the perspective of everyone involved in the scholarly communication chain, all of whom are adding value in one way or another (that's why we get paid!).  There really is no such thing as a free lunch, so trying to make research articles completely free - no matter how appealing that may be philosophically - is not a realistic option. Someone, somewhere will be paying for it, either overtly (eg through advertising or APCs) or covertly (eg, by selling personal data to other companies or by spending time publishing instead of researching).  However, there is huge disagreement about how much it costs to publish an article, from the $99 PeerJ membership model through to the $5200 it costs to publish in Nature.  And, as they say, if you pay peanuts you get monkeys (interestingly, PeerJ's logo is a monkey!) so your point about the quality of editing (including peer review) in OA journals is well made.  The last thing anyone wants is to have bad science freely available.  Peer review is not a perfect system, but most scientists believe it works most of the time. I don't believe that PLoS One is publishing bad science - as I understand it, their 'light' peer review simply means that reviewers don't assess articles based on novelty or fit, but only on whether they are scientifically sound. That enables them to charge considerably less for PLoS One ($1350)than for, say PLoS Biology ($2900), which has a more intensive peer review process, taking into account scientific importance as well as rigor. You also noted that not everyone can afford to pay an APC anyway - some disciplines, such as mathematics and physics, receive relatively little funding, and there are large parts of the world that can't afford to pay to publish at all (though many publishers reduce their prices in those cases). But lack of money should not disqualify researchers from publishing - and from publishing in the journal of their choice, not just the journal they can afford.  Nor should the relative cost of an APC be used to discourage scientists from publishing in their preferred journal.

Green OA is sometimes described as 'no one pays', however, it is becoming increasingly apparent that someone does (need to) pay, because – for now at least – green OA relies on the continuation of the subscription model to survive.  This is why the issue of embargo dates is so important - too short an embargo and there's a risk that libraries will cancel their subscription; too long and the whole point of making an article publicly available is lost. The jury is out on this issue too - no one really knows how short is too short, though it does seem very likely that this also varies by discipline. And how do you figure that out without jeopardizing the existence of the journals involved, not to mention the scholarly and scientific societies that support them?  One possible method is to use half life analysis, looking at how long it takes before an article has achieved half of all its lifetime views, which could help ascertain a 'safe' embargo period that will protect journal subscriptions. Another option is to allow authors to post an early version of their manuscript from the get go but, as you point out, that carries the risk of bad science escaping onto the web. Although scientists may understand the distinction between the accepted version of a paper and the final version, the general public probably does not.

My own personal feeling is that there is a lot to love about OA. It's revolutionizing all of scholarly communications and forcing everyone who is involved to think again about things we've long taken for granted - Impact Factors, tenure, peer review, publishing ethics, and more.  But at the same time, I worry that a little bit of knowledge can be a dangerous thing. The OA debate so far has been dominated by a relatively small number of loud voices from a relatively small number of disciplines and organizations, who are influencing some awfully big decisions that could have a significant impact on science and scientists, such as what license an author must sign (do all authors really want to sign away all their rights under a Creative Commons By Attribution (CC-BY) license?), how long an embargo period should be, whether green or gold OA is better.  We don't have all the answers to these questions yet and we need to do more to ensure that everyone's voice is heard in what I hope, going forward, will be a less polarized and more collaborative approach to solving these issues.

These views are my own and are not necessarily those of my employer

Thursday, June 20, 2013

Open Access - solid reasoning, or a bunch of hypothetical statements?

This post will be the first of a pair triplet on open access journals, which offer author's the ability to pay the publication fee in exchange for their article to be free to anyone wishing to read it. Here I will discuss whether open access stands up to its claims, and my mum will respond in the next post using highlights from Scholarly Kitchen, a publishing blog she contributes to. My grandfather, who is well-versed in science communication, will finish up the trio with his comments.

So, what is open access and why are people so obsessed with it? 

Scientists are increasingly jumping on the open access bandwagon for two major reasons, I think. The first (lesser-cited one) is that if journals are free and so more people can access them, that article is more likely to be cited, and more citations means more fame for the author and the institution, and possibly more funding (or accelerated tenure). The second reason is that the public, as well as scientists at smaller institutions, in under-developed countries, or independent scientists, should be able to have access to research without paying exorbitant fees.

Perhaps the greatest advocates for open access are the greatest consumers of knowledge - university libraries. These are the libraries which provide access to the literature upon which their most prominent researchers build and bring fame and money to the institution. However, these libraries face a dilemma - they must provide researchers with these articles, but the subscription costs for many journals are increasing faster than library budgets. Therefore, as long as open access journals offer the content researchers need, libraries have an opportunity to reduce costs. But these costs are then just diverted elsewhere in university budgets to pay for publishing articles. A quick Google Scholar search looking for "University of Massachusetts", "journal" and 2012 returns 16,000 articles published last year. If all of these were published in PLoS ONE, the largest open access journal in existence, then this would cost the university system $8,000,000, which is about one and a half times UMass Amherst's library materials budget. A saving to the university? Not quite. See, the fundamental issue is that library budgets have been a shrinking part of university budgets for the past 14 years, while money is diverted (at least at UMass) to buildings, bouncy castle parties, and other shows of grandeur which do little for learning and/or safety.
My new lab building to be at UMass. It instills an incredible sense of guilt associated with unnecessary destruction of historic buildings and materialism-driven construction of the new every time I look at it. Picture from

Returning to the idea of free articles being more available to the public, we must then ask why the public would want to be on the cutting edge of research. Many of these articles are difficult to understand, even for scientists, and the US government is moving towards making articles stemming from research it funds must be publicly available after one year (though I am unsure whether this is from the online pre-publishing date, which may be a year before the official online or paper printing date). There are clearly many potential customers for these free articles - imagine a mother looking for alternative treatments for their child's illness, or an environmentalist group looking to advise the government on climate policy - but it is difficult to determine how much making an article open access increases the audience size and breadth. It would be interesting to compare view counts for "normal" and open access articles in journals with publish a mix of both and see if the open access articles receive more views. Of course, it is possible that people who believe their article is more pertinent to the public may choose to write and fund their article in a way which will optimize public viewing, thereby biasing view count results. But a quick idea might be nice - anyone want to do that study?  

As a final point on the Open Access discussion, I would like to briefly mention that in theory some researchers are worried about publishing in Open Access journals because the quality of editing is lower. I don't necessarily think that the quality of editing is lower, but it is somewhat perverse that basically researchers are paying to have their research published, and only those with money can afford to do this. This isn't much of a worry for lab scientists, which often work with very large budgets, but physicists and many other disciplines work on much smaller budgets that cannot easily absorb a $500 publishing fee. That said, there are arguably other editing rules which potentially do greater harm to the literature and knowledge base than who has the most money - for example results in which no change or difference was observed between two groups are basically unpublishable. And PLos ONE takes the view that ultimately each reader should decide on the validity of an article for him or herself, and demonstrate support for work by citing it. However, if a journal like PLoS ONE produces articles with public-friendly descriptions of the research, and the science has fundamental technical or ethical flaws, they may not be able to detect the errors, and, becoming more like News of the World than the New York Times, bad science can spread through the unfiltered public conscience and become a social fact. Of course, poor editing is not limited to open access journals, but the fact that they are so openly available means that editing needs to be stricter for freely-available than subscription-only journals, I think.

What do you think?

Thursday, June 13, 2013

Rodents of Unusual Size and the (fire) Swamp

The "science"-related post I was working on needs a bit more time to mature, so I thought I would discuss my recent encounters with ROUS's. 

 The famed Fire Swamp scene from The Princess Bride

I am a bit of a sadist. As such, one of my favorite early morning distractions is to identify roadkill as I ride my bike to school. This is actually more challenging than you would think - the cars drive so fast on this road that the animals actually explode, and combined with the plethora of scavengers, carcass identification has to be made on just a joint or two. Or the smell. Rabbits definitely smell different to squirrels. Courtesy of my time at the Boston Area Climate Experiment, I can identify voles a mile off. I am still working on distinguishing between toad, frog, slug and earthworm smell.

But about a month ago, a fine piece of roadkill caught my attention. It was pretty fresh and the head was pretty intact. And it was quite possibly the scariest thing I have ever seen. Because when I looked on Wikipedia's mammals of Massachusetts page to reassure myself it wasn't in fact a rodent of unusual size, and that the pioneer valley is in fact a regular swamp, and not a Fire Swamp, my creature wasn't there. Nope. It was, in fact, a rodent of unusual size.

I managed to convince myself that it was some mutant creature, and since the mutation rate of most animals is very low, that there probably wouldn't be another one. Except earlier this week, there was. And it was alive and on the bike path less than four feet away from me. My bike has issues when squirrels happen to get tangled in my wheels - hitting a hissing, snarling, four-foot long rodent-kimodo dragon hybrid is another story. So luckily it waddled off, but I could see it in its eyes that it and/or its probably abundant progeny would be after me. My hopes of the roadkill being a rare mutant went out the window.

So I tried looking up this creature, once again, online. Surely someone must have seen a similarly giant rodent. But no - or if they had, they hadn't lived to tell the tail. And, as I rode home in the pitch black at the end of a very long day, that beast was still on the loose, waiting for me.

But the next morning, there was the freshest roadkill imaginable on the road. It was a Virginia opossum. Lying there, the blood trickling from its mouth, it was still the ugliest thing I have ever seen, but all of a sudden seemed only two feet long, and not as scraggly as before. 

Way handsomer in photos than in real life (

So, without spending lots of money to learn about psychology and/or buying any self-help magazines or time with a counsellor, here are the steps of fear: 1. something scary appears and you blow it out of proportion because it is 5am and you have nothing better to think about. This is how the Loch Ness monster was born. 2. you are convinced that it will get you (you impose what you wish to happen to it (ie for it to be eaten) as a wish the scary thing wants of you). 3. you see the scary thing again, contextualize it, and it seems less scary. This is desensitization. This is also why we need solid research and repeated observations against a larger body of evidence before we draw conclusions. Science. 

So, how about some fun facts about opossums:

Opossums are not rodents, but rather marsupials, like kangaroos. This means that their babies are born tiny (about a tenth of a gram) and have to crawl into their mother's pouch to finish gestation. This also means that their closest relatives live in the southern hemisphere - when Pangea (the last super continent) broke up, their ancestors in the northern hemisphere died out, and they evolved somewhat in isolation over the next millions of years. Opossums came from south and central America when South America met North America about three million years ago (and before the Panama Canal separated the two again), but didn't really explode and spread as far north as they exist now until Europeans colonized. Virginia opossums, the most successful and widespread kind of opossum, have relatively sparse fur and therefore pretty terrible when it comes to the cold, but the arrival of settlers and their warm houses has enabled them to spread into southern Canada. These northern opossums have denser fur and much larger than their southern tropical relatives. 

Imagine if you had tens of these bursting out your belly. Best incentive ever for a tummy tuck.

Despite the fact that opossums are famous for playing 'possum (dead), this is actually a pretty rare behaviour - they are more likely to hiss, tail lash, climb, swim, or run at a whopping speed of up to 7 km/hr. This antisocial behaviour means that they don't really hang out with other opossums except for mating (for which they only get one year in before they die, usually). This is fortunate because they are unlikely to form a gang and chase me down the street. 

Opossums are also supposed to be nocturnal, which, since I thought I was going to school during the daytime, apparently means I need to go later. They are omnivores, and eat pretty much anything, by all accounts. Like the chickens which were going beserk on my way to school this morning. Opossums do have predators, but maybe not as much in New England as in the south, where 'possum makes a tasty pie (I think I like this possum pie better). They are resistant to the venom of quite a lot of snakes, but may be consumed by brave domestic dogs, owls, coyotes, and racoons (none of which I would like to see on my bike path either, thank you very much).
including owls, domestic dogs, coyotes, red foxes, raccoons, bobcats and large snakes, among others. They may also be hunted or trapped by humans. Virginia opossums are immune to the venom of a variety of snakes from Family Viperidae including eastern and western diamondback rattlesnakes, copperheads, cottonmouth moccasins and Korean mamusi. This species may have a better chance of survival with

Friday, June 7, 2013

Eureka part two!

OK, so I have my plan for entertaining the Eureka! girls (see previous post), and have decided that since we will potentially be getting these girls again and again, I should probably think about how this fits into the bigger picture. I will discuss it in more detail in a future post, but I thought first I would talk a little more about the process involved in making it.

In making my educational plan (complete with expected learning outcomes and everything, which makes me feel like a real live teacher), I had to follow a set of SMART guidelines provided by Girls, Inc. I wish I could share the complete document here, but I can't. Anyway, most of these are things that would be nice for any curriculum - make it interactive, don't spoon feed the kids answers, let them use expensive toys they probably won't have access to at home, and make it relevant to something in their lives. But other guidelines are explicitly designed to push the fact that girls can do boy things, and shouldn't do "girl" things, which I disprove of. For example, we are supposed to conclude with a discussion of what boys would say if they saw girls doing the activity. We aren't supposed to include large sections of cutting, colouring, cooking or sewing - all incredibly vital components of lab work - because they are traditional female activities (even though I am sure most people of both sexes could work on these skills). We are also supposed to frown upon behaviours such as saying things are icky, even though some things really are icky to people, independent of their gender. So basically, the guidelines are telling me I can't express human emotions in response to things I am working with; when I found a vole that had fallen into a bucket of water and had been replaced by a wriggling writhing mass of maggots and the most offensive stench imaginable, I should have thought it was delightful. I guess I'm a pansy then, and telling me I'm pathetic will magically make me strong, smart and bold (R).

So I guess the second step in developing a class proposal was to overcome some of my anger with the underlying assumptions of the science camp program. While I support the idea that girls should have access to more science, I don't think it should be because they are girls. Maybe getting more girls involved means they are more likely to find a friend of the same sex interested in the same thing, but to say that boys don't let girls do things and girls let them get away with it is an insult to both sexes. Maybe I just don't understand because I was always told to do what I wanted and thought was right, and not care what other people might think. It is unimaginable to me that anyone would not do something because they thought it was a boy's or a girl's job. As Nike says, "just do it" (or as I constantly tell myself, shut up and get on with it).

What we need now is a cooking, cleaning, sewing, and make-up school that we assume boys will find interesting, exclude girls from applying, and brainwash the boys into believing that their biggest dream is to be a makeup artist, and if they don't want that, there is something wrong with them.

Tuesday, June 4, 2013

Eureka! Someone else had an idea

This summer, UMass is collaborating with Girls, Inc. of Holyoke to host 30 girls in a Eureka! camp, which is basically a five week program to try and get girls into science and technology. What is special about this summer program is first that it is looking for B and C  - not A - students to participate, second that it is taking kids from an area where the high school graduation rate hovers around 50%, and third, that the kids (and parents) signing on do so for five summers, with continued programming in the school year. 

Moo ha ha ha - you are chained in to science for the next five years! (you have no idea how many inapropriate pictures I had to go through on google images to get to this one). Image courtesy of

So, put in front of a group of 13 year olds, what do you try and teach them? How do you make it relevant, and keep them engaged? Ignore stereotypes about female teen preferences, I hope.

The first task was to learn about the state science curriculum for seventh and eighth graders to see what they should know and/or be doing in school at this time. It hasn't been updated for seven years, though, which means it doesn't account for such life-altering knowledge such as the fact that humans and neanderthals probably mated (therefore explaining the peculiar morphology of the Pold skull), or that, like us,  bacteria have adaptive immune systems (ie they can mount invader-specific responses as a result of remembering the suite of invaders they or their ancestors have previously faced). But basically the state science curriculum tells us to let the students start to do hypothesis-driven work. That seems like a well, duh statement that should invite questions about how younger children do science if they don't make hypotheses. But somehow, various researchers studying microbial ecology seem to take almost exclusively exploratory approaches to their work. So anyway - we should promote classical science.

The second task was to learn what these girls think about, so that we can make the class relevant. This dragged up a very long discussion about middle school. Awkward. Why would you ever want to talk about those years of terror. You know what was going through my mind at that time? How pathetic and immature my peers were for forming cliques. That hasn't changed much - to a certain extent, scientists never grow out of middle school. Many of them are still fundamentally insecure and bitter, some of them want to be everyone's friend, and some of them want to have all the latest toys, no matter the cost. Scientists have cliques, teenage girls have cliques. Perfect match.

Look! Amorphous clone meets similarly amorphous clone and makes one happy clique. Image courtesy of

The final task was to figure out what to teach them. My PI and I decided that getting them to collect soil from their yard or a park near their house (or somewhere on the UMass campus) and getting them to compare carbon dioxide emissions and the number of cells in a gram of soil might be a good idea. We would teach them about how lots of microbes are generally found where there is a lot of carbon, and how there is more carbon in forest soil than soil around a street tree, and ask them to predict which soil will have the most microbes and/or the highest level of carbon dioxide production. We would then tie back into climate change and land use change in the context of greening abandoned lots (of which the Peter Pan bus between Springfield and UMass assured me there were many).

But do you think middle school girls can connect to soil, climate change, and land use change? How could soil inspire you?